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Question: ANNOVAR Annotate VCF tool not working
1
gravatar for priyarashz
19 months ago by
priyarashz • 10
priyarashz • 10 wrote:

Hi, I tried using the ANNOVAR annotate VCF tool and got the following output

empty formatvcfdatabasehg19 Log: tool progress Log: tool progress Unknown option: vcfinput Usage: table_annovar.pl [arguments] <query-file> <database-location>

Kindly help me.
galaxy • 454 views
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modified 19 months ago by Jennifer Hillman Jackson ♦ 25k • written 19 months ago by priyarashz • 10

Hello - It looks like you sent in a bug report as well. We'll review and get back to you about how to resolve the issue. Thanks! Jen, Galaxy team

ADD REPLY • link written 19 months ago by Jennifer Hillman Jackson ♦ 25k
0
gravatar for Jennifer Hillman Jackson
19 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

This is a true bug. It is not clear yet if the problem is with how the tool was installed or if there is a problem with the tool wrapper itself. Details here: https://github.com/galaxyproject/galaxy/issues/4001

The current workaround is to use the prior version, 0.1, also available for use at http://usegalaxy.org.

Thank you for reporting the problem and for sharing your example history! Jen, Galaxy team
ADD COMMENT • link written 19 months ago by Jennifer Hillman Jackson ♦ 25k
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